OK got that trace and found the problem. The patch below should fix it,
I will commit it now. The issue is that blktrace (on the kernel side)
can send out notices, telling you about a process or the time mapping.
The fio blktrace loader just needs to discard such messages, right now
it got intepreted it as a normal trace and do random things. What
happened with this trace was that the delay from the previous notice was
seen as really huge, so fio was just sleeping waiting for that time to
pass.